Report last updated Mon May 23 19:08:37 2016.
Exploratory analysis
In this section we will see descriptive figures about quality of the data, reads with adapter, reads mapped to miRNAs, reads mapped to other small RNAs.
size distribution
After adapter removal, we can plot the size distribution of the small RNAs.
miRNA
total miRNA expression annotated with mirbase
Distribution of mirna expression
cumulative distribution of miRNAs
Clustering
MDS plot
complexity
Number of miRNAs with > 3 counts.
| colSums(counts > 10) | |
|---|---|
| A201_Day0 | 348 |
| A200_Day0 | 380 |
| A196_Day0 | 363 |
| A190_Day28 | 389 |
| A189_Day14 | 374 |
| A181_Day7 | 380 |
| A180_Day7 | 420 |
| A178_Day3 | 399 |
| A172_Day2 | 387 |
| A167_Day1 | 338 |
| A165_Day1 | 369 |
| A89_Day28 | 365 |
| A86_Day28 | 376 |
| A85_Day14 | 355 |
| A84_Day14 | 394 |
| A80_Day7 | 392 |
| A75_Day3 | 373 |
| A74_Day3 | 409 |
| A70_Day2 | 430 |
| A69_Day2 | 423 |
| A63_Day1 | 372 |
novel miRNA by mirdeep2
total miRNA expression
Distribution of mirna expression
cumulative distribution of miRNAs
Clustering
MDS plot
complexity
Number of miRNAs with > 3 counts.
| colSums(counts > 10) | |
|---|---|
| A201_Day0 | 75 |
| A200_Day0 | 93 |
| A196_Day0 | 82 |
| A190_Day28 | 87 |
| A189_Day14 | 80 |
| A181_Day7 | 88 |
| A180_Day7 | 103 |
| A178_Day3 | 91 |
| A172_Day2 | 90 |
| A167_Day1 | 71 |
| A165_Day1 | 86 |
| A89_Day28 | 76 |
| A86_Day28 | 85 |
| A85_Day14 | 73 |
| A84_Day14 | 86 |
| A80_Day7 | 79 |
| A75_Day3 | 78 |
| A74_Day3 | 94 |
| A70_Day2 | 107 |
| A69_Day2 | 102 |
| A63_Day1 | 87 |
Others small RNA
The data was analyzed with seqcluster
This tools used all reads, uniquely mapped and multi-mapped reads. The first step is to cluster sequences in all locations they overlap. The second step is to create meta-clusters: is the unit that merge all clusters that share the same sequences. This way the output are meta-clusters, common sequences that could come from different region of the genome.
genome covered
In this table 1 means % of the genome with at least 1 read, and 0 means % of the genome without reads.
The normal value for human data with strong small RNA signal is: 0.0002. This will change for smaller genomes.
classification
Number of reads in the data after each step:
- raw: initial reads
- cluster: after cluster detection
- multimap: after meta-cluster detection
Check complex meta-clusters: This kind of events happen when there are small RNA over the whole genome, and all repetitive small rnas map to thousands of places and sharing many sequences in many positions. If any meta-cluster is > 40% of the total data, maybe it is worth to add some filters like: minimum number of counts -e or --min--shared in seqcluster prepare
A201_Day0 A200_Day0 A196_Day0 A190_Day28 A189_Day14 A181_Day7
A180_Day7 A178_Day3 A172_Day2 A167_Day1 A165_Day1 A89_Day28 A86_Day28
A85_Day14 A84_Day14 A80_Day7 A75_Day3 A74_Day3 A70_Day2 A69_Day2
A63_Day1complexity
Number of miRNAs with > 10 counts.
| colSums(clus_ma > 10) | |
|---|---|
| A201_Day0 | 536 |
| A200_Day0 | 545 |
| A196_Day0 | 559 |
| A190_Day28 | 556 |
| A189_Day14 | 555 |
| A181_Day7 | 554 |
| A180_Day7 | 564 |
| A178_Day3 | 574 |
| A172_Day2 | 546 |
| A167_Day1 | 547 |
| A165_Day1 | 577 |
| A89_Day28 | 536 |
| A86_Day28 | 561 |
| A85_Day14 | 578 |
| A84_Day14 | 563 |
| A80_Day7 | 553 |
| A75_Day3 | 564 |
| A74_Day3 | 550 |
| A70_Day2 | 562 |
| A69_Day2 | 563 |
| A63_Day1 | 559 |
Contribution by class
Differential expression
DESeq2 is used for this analysis.
Analysis for miRNA
## Comparison: fa_model_mirna {.tabset}
out of 645 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up) : 163, 25%
LFC < 0 (down) : 133, 21%
outliers [1] : 1, 0.16%
low counts [2] : 88, 14%
(mean count < 1)
[1] see ‘cooksCutoff’ argument of ?results
[2] see ‘independentFiltering’ argument of ?results
NULL
Differential expression file at: fa_model_mirna.tsv
Normalized counts matrix file at: fa_model_mirna_log2_counts.tsv
MA plot plot
Volcano plot
QC for DE genes p-values/variance
Most significand, FDR< 0.05 and log2FC > 1 : 119
Plots most significand
Plot top 9 genes
Top DE genes
| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | symbol | description | Day14vsDay0 | Day1vsDay0 | Day2vsDay0 | Day3vsDay0 | Day7vsDay0 | absMaxLog2FC | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| mmu-miR-21a-3p | 3349.90195 | 0.2092341 | 0.2123191 | 373.2788 | 0 | 0 | mmu-miR-21a-3p | mmu-miR-21a-3p | 1.2023999 | 2.6461098 | 3.1643137 | 2.7118794 | 2.2483118 | 3.1643137 |
| mmu-miR-21a-5p | 235757.69370 | 0.5885233 | 0.1674390 | 323.3068 | 0 | 0 | mmu-miR-21a-5p | mmu-miR-21a-5p | 1.5993843 | 2.0354839 | 2.4120192 | 2.3303773 | 2.3425021 | 2.4120192 |
| mmu-miR-92a-1-5p | 139.77162 | -0.1588406 | 0.1761096 | 293.8874 | 0 | 0 | mmu-miR-92a-1-5p | mmu-miR-92a-1-5p | 0.3916372 | 1.5100673 | 1.6814937 | 1.2625307 | 0.8592778 | 1.6814937 |
| mmu-miR-181c-5p | 5177.32928 | 0.7730872 | 0.1141849 | 270.6441 | 0 | 0 | mmu-miR-181c-5p | mmu-miR-181c-5p | 0.6225336 | -0.4106138 | -0.4550042 | -0.5910839 | 0.1610376 | 0.6225336 |
| mmu-miR-375-3p | 1831.43198 | 0.6415690 | 0.1500521 | 249.5976 | 0 | 0 | mmu-miR-375-3p | mmu-miR-375-3p | 1.5341903 | 0.2266603 | 1.1013174 | 1.5199590 | 1.7979345 | 1.7979345 |
| mmu-miR-130b-3p | 121.24753 | 0.9038785 | 0.2313726 | 235.2099 | 0 | 0 | mmu-miR-130b-3p | mmu-miR-130b-3p | 1.8024114 | 0.7083430 | 1.6076363 | 2.4460588 | 2.4122506 | 2.4460588 |
| mmu-miR-199a-5p | 1494.91668 | 1.1819872 | 0.1614447 | 225.4967 | 0 | 0 | mmu-miR-199a-5p | mmu-miR-199a-5p | 1.7951627 | 0.2449684 | 0.5223752 | 1.0193132 | 1.7315863 | 1.7951627 |
| mmu-miR-199a-3p | 15543.36157 | 1.1521346 | 0.1641965 | 216.1439 | 0 | 0 | mmu-miR-199a-3p | mmu-miR-199a-3p | 1.6577361 | 0.0145188 | 0.1361008 | 0.6047284 | 1.4022824 | 1.6577361 |
| mmu-miR-199b-3p | 15532.96146 | 1.1525354 | 0.1642081 | 216.0259 | 0 | 0 | mmu-miR-199b-3p | mmu-miR-199b-3p | 1.6577379 | 0.0150815 | 0.1362317 | 0.6042545 | 1.4016804 | 1.6577379 |
| mmu-miR-146b-5p | 1879.08619 | 1.6373420 | 0.2285428 | 211.7384 | 0 | 0 | mmu-miR-146b-5p | mmu-miR-146b-5p | 2.8223531 | 1.1898393 | 1.5489137 | 2.6665250 | 2.7112640 | 2.8223531 |
| mmu-miR-181a-5p | 79471.80435 | 0.4281674 | 0.1028707 | 206.5081 | 0 | 0 | mmu-miR-181a-5p | mmu-miR-181a-5p | 0.2454838 | -0.4277786 | -0.5874128 | -0.6785543 | -0.3003926 | 0.6785543 |
| mmu-miR-15b-5p | 444.43295 | 0.1121891 | 0.1380392 | 204.4162 | 0 | 0 | mmu-miR-15b-5p | mmu-miR-15b-5p | 0.5679018 | 0.4463544 | 0.9437916 | 1.3881331 | 1.2517012 | 1.3881331 |
| mmu-let-7j | 3660.48447 | 0.7473125 | 0.1423042 | 191.9095 | 0 | 0 | mmu-let-7j | mmu-let-7j | 1.4174612 | 0.2660367 | 0.5022776 | 1.0472989 | 1.5061737 | 1.5061737 |
| mmu-miR-18a-5p | 140.48080 | 0.2058626 | 0.2645325 | 189.7141 | 0 | 0 | mmu-miR-18a-5p | mmu-miR-18a-5p | 1.0554008 | 1.6065388 | 2.2486953 | 2.4126605 | 2.0513531 | 2.4126605 |
| mmu-miR-298-5p | 63.44882 | 1.9510187 | 0.4342741 | 189.7205 | 0 | 0 | mmu-miR-298-5p | mmu-miR-298-5p | 3.0350291 | 1.0633386 | 3.1482262 | 4.0225210 | 3.8880722 | 4.0225210 |
| mmu-miR-132-3p | 995.91587 | 1.0972911 | 0.2259190 | 183.9388 | 0 | 0 | mmu-miR-132-3p | mmu-miR-132-3p | 2.3521595 | 2.3004948 | 2.4792479 | 2.5213285 | 2.6462390 | 2.6462390 |
| mmu-let-7i-5p | 28002.55133 | 0.6010586 | 0.1546107 | 178.5984 | 0 | 0 | mmu-let-7i-5p | mmu-let-7i-5p | 1.3966011 | 0.9385165 | 1.4164715 | 1.6881308 | 1.7028061 | 1.7028061 |
| mmu-miR-221-3p | 5762.96983 | -0.0016366 | 0.0879878 | 167.2031 | 0 | 0 | mmu-miR-221-3p | mmu-miR-221-3p | 0.2406472 | 0.8688996 | 0.6301371 | 0.5365345 | 0.3439440 | 0.8688996 |
| mmu-miR-214-3p | 671.15060 | 1.1800627 | 0.2515532 | 163.6752 | 0 | 0 | mmu-miR-214-3p | mmu-miR-214-3p | 2.2324322 | 0.5469246 | 1.6893764 | 2.4875904 | 2.4306447 | 2.4875904 |
| mmu-miR-223-3p | 588.88017 | 1.1182354 | 0.2385065 | 160.3819 | 0 | 0 | mmu-miR-223-3p | mmu-miR-223-3p | 1.7473818 | 1.8978195 | 2.2931158 | 2.5513986 | 2.6457617 | 2.6457617 |
Working with 119 genes 
Analysis for novel miRNA
## Comparison: fa_model_novel {.tabset}
out of 255 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up) : 35, 14%
LFC < 0 (down) : 21, 8.2%
outliers [1] : 3, 1.2%
low counts [2] : 45, 18%
(mean count < 1)
[1] see ‘cooksCutoff’ argument of ?results
[2] see ‘independentFiltering’ argument of ?results
NULL
Differential expression file at: fa_model_novel.tsv
Normalized counts matrix file at: fa_model_novel_log2_counts.tsv
MA plot plot
Volcano plot
QC for DE genes p-values/variance
Most significand, FDR< 0.05 and log2FC > 1 : 28
Plots most significand
Plot top 9 genes
Top DE genes
| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | symbol | description | Day14vsDay0 | Day1vsDay0 | Day2vsDay0 | Day3vsDay0 | Day7vsDay0 | absMaxLog2FC | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| mmu-chr2_1617-5p | 15704.04826 | 1.2477818 | 0.1746373 | 209.52844 | 0e+00 | 0.0e+00 | mmu-chr2_1617-5p | mmu-chr2_1617-5p | 1.7027375 | 0.0082195 | 0.0858072 | 0.5345992 | 1.4062735 | 1.7027375 |
| mmu-chr2_1617-3p | 1604.50416 | 1.2688125 | 0.1741413 | 202.95721 | 0e+00 | 0.0e+00 | mmu-chr2_1617-3p | mmu-chr2_1617-3p | 1.8256632 | 0.2348821 | 0.4584559 | 0.9290956 | 1.7115133 | 1.8256632 |
| mmu-chr19_17788-5p | 1870.89106 | 1.7255196 | 0.2440247 | 183.76794 | 0e+00 | 0.0e+00 | mmu-chr19_17788-5p | mmu-chr19_17788-5p | 2.8532472 | 1.1836523 | 1.4959106 | 2.5986829 | 2.7055385 | 2.8532472 |
| mmu-chr10_11097-5p | 28102.83066 | 0.6957317 | 0.1572774 | 158.46900 | 0e+00 | 0.0e+00 | mmu-chr10_11097-5p | mmu-chr10_11097-5p | 1.4408854 | 0.9261011 | 1.3499184 | 1.6070990 | 1.6992468 | 1.6992468 |
| mmu-chr1_555-5p | 667.46643 | 1.2691971 | 0.2622320 | 146.04206 | 0e+00 | 0.0e+00 | mmu-chr1_555-5p | mmu-chr1_555-5p | 2.2758244 | 0.5344898 | 1.6321099 | 2.4187867 | 2.4222843 | 2.4222843 |
| mmu-chr13_13968-5p | 61.65890 | -0.3566850 | 0.2542023 | 138.44277 | 0e+00 | 0.0e+00 | mmu-chr13_13968-5p | mmu-chr13_13968-5p | -0.0269858 | 1.1506837 | 1.5581120 | 0.8687753 | 0.9284907 | 1.5581120 |
| mmu-chr1_555-3p | 115.13914 | 1.3546718 | 0.2391823 | 116.86146 | 0e+00 | 0.0e+00 | mmu-chr1_555-3p | mmu-chr1_555-3p | 1.8908435 | 0.2770808 | 1.0133671 | 1.4400643 | 1.8729387 | 1.8908435 |
| mmu-chr11_11842-5p | 1382.93118 | 0.9296450 | 0.2507180 | 98.17101 | 0e+00 | 0.0e+00 | mmu-chr11_11842-5p | mmu-chr11_11842-5p | 1.0489480 | -0.6201143 | -0.8844405 | -0.0090860 | 0.3996378 | 1.0489480 |
| mmu-chr4_4731-5p | 639.48337 | 1.5006912 | 0.2233972 | 86.16079 | 0e+00 | 0.0e+00 | mmu-chr4_4731-5p | mmu-chr4_4731-5p | 1.7109593 | 1.5824969 | 1.8862033 | 1.8008005 | 1.9147657 | 1.9147657 |
| mmu-chr7_7254-3p | 62.05451 | 0.7366221 | 0.2251416 | 84.25959 | 0e+00 | 0.0e+00 | mmu-chr7_7254-3p | mmu-chr7_7254-3p | 0.7659992 | 0.9640480 | 1.2852468 | 1.6636096 | 1.0832762 | 1.6636096 |
| mmu-chr11_11562-5p | 7094.45722 | 0.2026164 | 0.0778748 | 83.73320 | 0e+00 | 0.0e+00 | mmu-chr11_11562-5p | mmu-chr11_11562-5p | 0.2720386 | -0.1950919 | -0.2988935 | -0.1130372 | -0.0034623 | 0.2988935 |
| mmu-chrX_18627-3p | 777.30582 | -0.0683547 | 0.1333196 | 71.97971 | 0e+00 | 0.0e+00 | mmu-chrX_18627-3p | mmu-chrX_18627-3p | -0.4616503 | -0.6040915 | -0.6853519 | -0.8646916 | -0.6407676 | 0.8646916 |
| mmu-chr4_4731-3p | 11.64074 | 5.5864065 | 1.2446180 | 71.53433 | 0e+00 | 0.0e+00 | mmu-chr4_4731-3p | mmu-chr4_4731-3p | 5.9332551 | 5.8722774 | 6.1835144 | 5.3788624 | 6.9622301 | 6.9622301 |
| mmu-chr14_14324-5p | 650.20373 | 0.1321476 | 0.1342842 | 69.72374 | 0e+00 | 0.0e+00 | mmu-chr14_14324-5p | mmu-chr14_14324-5p | 0.2733892 | 0.8354807 | 0.6416453 | 0.5808258 | 0.7394271 | 0.8354807 |
| mmu-chr12_13064-5p | 242.72311 | -0.2393021 | 0.2138295 | 61.63439 | 0e+00 | 0.0e+00 | mmu-chr12_13064-5p | mmu-chr12_13064-5p | -0.7873948 | -0.1124744 | -0.6147547 | -0.8729946 | -1.4391207 | 1.4391207 |
| mmu-chr7_7254-5p | 352.21891 | 0.1637386 | 0.1375269 | 59.25820 | 0e+00 | 0.0e+00 | mmu-chr7_7254-5p | mmu-chr7_7254-5p | 0.3285514 | 0.1666189 | 0.5267945 | 0.7043941 | 0.7707181 | 0.7707181 |
| mmu-chr8_8358-5p | 11893.87663 | -0.6576385 | 0.5002037 | 55.69714 | 0e+00 | 0.0e+00 | mmu-chr8_8358-5p | mmu-chr8_8358-5p | -0.8809473 | 1.1651061 | 1.5080060 | -1.0549920 | -0.7001651 | 1.5080060 |
| mmu-chr11_11568-3p | 605.58914 | 0.3205571 | 0.1255872 | 46.53153 | 0e+00 | 3.0e-07 | mmu-chr11_11568-3p | mmu-chr11_11568-3p | 0.3391268 | -0.1641964 | -0.1565013 | -0.2148585 | 0.2693321 | 0.3391268 |
| mmu-chr18_17508-5p | 371.97170 | -0.3588681 | 0.1276606 | 42.78688 | 1e-07 | 1.4e-06 | mmu-chr18_17508-5p | mmu-chr18_17508-5p | -0.6669813 | -0.2609442 | -0.4787330 | -0.5794412 | -0.6441856 | 0.6669813 |
| mmu-chr8_9013-5p | 139.09155 | -0.1207145 | 0.2029023 | 40.54146 | 4e-07 | 3.7e-06 | mmu-chr8_9013-5p | mmu-chr8_9013-5p | -1.1053441 | -0.0885767 | -0.1244822 | 0.0506256 | -0.5256979 | 1.1053441 |
Working with 28 genes 
Analysis for isomiRs
## Comparison: fa_model_isomir {.tabset}
out of 9976 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up) : 1140, 11%
LFC < 0 (down) : 906, 9.1%
outliers [1] : 1, 0.01%
low counts [2] : 3095, 31%
(mean count < 1)
[1] see ‘cooksCutoff’ argument of ?results
[2] see ‘independentFiltering’ argument of ?results
NULL
Differential expression file at: fa_model_isomir.tsv
Normalized counts matrix file at: fa_model_isomir_log2_counts.tsv
MA plot plot
Volcano plot
QC for DE genes p-values/variance
Most significand, FDR< 0.05 and log2FC > 1 : 1071
Plots most significand
Plot top 9 genes
Top DE genes
| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | symbol | description | Day14vsDay0 | Day1vsDay0 | Day2vsDay0 | Day3vsDay0 | Day7vsDay0 | absMaxLog2FC | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| mmu-miR-21a-5p.iso.t5:0.t3:C.ad:C.mm:0 | 11278.35779 | 0.2023678 | 0.2104789 | 544.8132 | 0 | 0 | mmu-miR-21a-5p.iso.t5:0.t3:C.ad:C.mm:0 | mmu-miR-21a-5p.iso.t5:0.t3:C.ad:C.mm:0 | 1.1912110 | 3.5583135 | 3.6269413 | 3.1720696 | 2.5279801 | 3.6269413 |
| mmu-miR-21a-5p.iso.t5:A.t3:0.ad:0.mm:0 | 846.80622 | 0.1694778 | 0.1776450 | 531.5104 | 0 | 0 | mmu-miR-21a-5p.iso.t5:A.t3:0.ad:0.mm:0 | mmu-miR-21a-5p.iso.t5:A.t3:0.ad:0.mm:0 | 1.3519726 | 2.1691581 | 2.8615896 | 2.8224250 | 2.4868270 | 2.8615896 |
| mmu-miR-21a-5p.iso.t5:0.t3:C.ad:A.mm:0 | 5274.01122 | -0.0478811 | 0.1617310 | 515.1055 | 0 | 0 | mmu-miR-21a-5p.iso.t5:0.t3:C.ad:A.mm:0 | mmu-miR-21a-5p.iso.t5:0.t3:C.ad:A.mm:0 | 0.9437825 | 1.9337577 | 2.6396474 | 2.4719199 | 2.0068352 | 2.6396474 |
| mmu-miR-21a-5p.iso.t5:A.t3:C.ad:0.mm:0 | 58.20176 | -0.3647279 | 0.4794563 | 467.9483 | 0 | 0 | mmu-miR-21a-5p.iso.t5:A.t3:C.ad:0.mm:0 | mmu-miR-21a-5p.iso.t5:A.t3:C.ad:0.mm:0 | 1.4586001 | 3.6699715 | 4.0272885 | 3.7082023 | 2.9310927 | 4.0272885 |
| mmu-miR-93-5p.ref.t5:0.t3:0.ad:0.mm:0 | 1410.00405 | 0.1081940 | 0.0882399 | 444.6899 | 0 | 0 | mmu-miR-93-5p.ref.t5:0.t3:0.ad:0.mm:0 | mmu-miR-93-5p.ref.t5:0.t3:0.ad:0.mm:0 | 0.4904528 | 0.6303569 | 1.1226739 | 1.3333864 | 1.1243616 | 1.3333864 |
| mmu-miR-21a-5p.iso.t5:0.t3:CT.ad:0.mm:0 | 64309.70315 | 0.2910704 | 0.1757690 | 444.2239 | 0 | 0 | mmu-miR-21a-5p.iso.t5:0.t3:CT.ad:0.mm:0 | mmu-miR-21a-5p.iso.t5:0.t3:CT.ad:0.mm:0 | 1.3727513 | 2.4099209 | 2.7935148 | 2.7337894 | 2.4797689 | 2.7935148 |
| mmu-miR-146b-5p.iso.t5:0.t3:G.ad:0.mm:0 | 542.44226 | 1.6358763 | 0.1742347 | 414.0365 | 0 | 0 | mmu-miR-146b-5p.iso.t5:0.t3:G.ad:0.mm:0 | mmu-miR-146b-5p.iso.t5:0.t3:G.ad:0.mm:0 | 2.6926429 | 0.5428686 | 1.1670029 | 2.3111355 | 2.5424858 | 2.6926429 |
| mmu-miR-199a-3p.iso.t5:0.t3:0.ad:A.mm:0 | 620.98234 | 1.5142002 | 0.1553404 | 397.0422 | 0 | 0 | mmu-miR-199a-3p.iso.t5:0.t3:0.ad:A.mm:0 | mmu-miR-199a-3p.iso.t5:0.t3:0.ad:A.mm:0 | 2.1517905 | 0.1785731 | 0.2175869 | 0.7617868 | 1.8248843 | 2.1517905 |
| mmu-miR-199b-3p.iso.t5:0.t3:0.ad:A.mm:0 | 620.98234 | 1.5142002 | 0.1553404 | 397.0422 | 0 | 0 | mmu-miR-199b-3p.iso.t5:0.t3:0.ad:A.mm:0 | mmu-miR-199b-3p.iso.t5:0.t3:0.ad:A.mm:0 | 2.1517905 | 0.1785731 | 0.2175869 | 0.7617868 | 1.8248843 | 2.1517905 |
| mmu-miR-21a-3p.iso.t5:c.t3:T.ad:0.mm:0 | 423.66178 | 0.0801993 | 0.2469328 | 377.9940 | 0 | 0 | mmu-miR-21a-3p.iso.t5:c.t3:T.ad:0.mm:0 | mmu-miR-21a-3p.iso.t5:c.t3:T.ad:0.mm:0 | 1.0153445 | 2.7914134 | 3.3196679 | 2.8470052 | 2.2915384 | 3.3196679 |
| mmu-miR-21a-5p.iso.t5:0.t3:C.ad:0.mm:0 | 65864.48117 | 0.2671976 | 0.2322570 | 368.7898 | 0 | 0 | mmu-miR-21a-5p.iso.t5:0.t3:C.ad:0.mm:0 | mmu-miR-21a-5p.iso.t5:0.t3:C.ad:0.mm:0 | 1.5005346 | 3.0306639 | 3.4940082 | 3.1911338 | 2.6853264 | 3.4940082 |
| mmu-miR-21a-3p.ref.t5:0.t3:c.ad:0.mm:0 | 1870.15869 | 0.1013924 | 0.2392049 | 357.4214 | 0 | 0 | mmu-miR-21a-3p.ref.t5:0.t3:c.ad:0.mm:0 | mmu-miR-21a-3p.ref.t5:0.t3:c.ad:0.mm:0 | 1.0332505 | 2.7361909 | 3.3841446 | 2.9207550 | 2.2230688 | 3.3841446 |
| mmu-miR-92a-1-5p.ref.t5:0.t3:0.ad:0.mm:0 | 135.00995 | -0.1503253 | 0.1701043 | 345.2868 | 0 | 0 | mmu-miR-92a-1-5p.ref.t5:0.t3:0.ad:0.mm:0 | mmu-miR-92a-1-5p.ref.t5:0.t3:0.ad:0.mm:0 | 0.4095784 | 1.4553068 | 1.7380425 | 1.4271687 | 0.9668157 | 1.7380425 |
| mmu-miR-181c-5p.iso.t5:0.t3:T.ad:0.mm:0 | 1523.53821 | 0.8405588 | 0.1209044 | 338.0922 | 0 | 0 | mmu-miR-181c-5p.iso.t5:0.t3:T.ad:0.mm:0 | mmu-miR-181c-5p.iso.t5:0.t3:T.ad:0.mm:0 | 1.0765788 | -0.4191428 | -0.3580316 | -0.2513222 | 0.7990521 | 1.0765788 |
| mmu-miR-181a-5p.iso.t5:0.t3:T.ad:0.mm:0 | 1668.80801 | 0.3241937 | 0.1003742 | 331.6893 | 0 | 0 | mmu-miR-181a-5p.iso.t5:0.t3:T.ad:0.mm:0 | mmu-miR-181a-5p.iso.t5:0.t3:T.ad:0.mm:0 | 0.6717940 | -0.6926857 | -0.5537966 | 0.2590926 | 0.6694544 | 0.6926857 |
| mmu-miR-21a-5p.iso.t5:0.t3:C.ad:G.mm:0 | 296.58796 | 0.2817179 | 0.2277302 | 317.3796 | 0 | 0 | mmu-miR-21a-5p.iso.t5:0.t3:C.ad:G.mm:0 | mmu-miR-21a-5p.iso.t5:0.t3:C.ad:G.mm:0 | 1.5396964 | 2.3395675 | 2.7828531 | 2.7714881 | 2.2489409 | 2.7828531 |
| mmu-miR-21a-5p.iso.t5:A.t3:CT.ad:0.mm:0 | 76.52812 | 0.9297556 | 0.3853488 | 317.1316 | 0 | 0 | mmu-miR-21a-5p.iso.t5:A.t3:CT.ad:0.mm:0 | mmu-miR-21a-5p.iso.t5:A.t3:CT.ad:0.mm:0 | 1.9237260 | 3.5530122 | 3.8607423 | 3.7776356 | 3.2155839 | 3.8607423 |
| mmu-miR-21a-5p.ref.t5:0.t3:0.ad:0.mm:0 | 74058.19837 | 0.7161811 | 0.1692574 | 311.4091 | 0 | 0 | mmu-miR-21a-5p.ref.t5:0.t3:0.ad:0.mm:0 | mmu-miR-21a-5p.ref.t5:0.t3:0.ad:0.mm:0 | 1.7579095 | 0.6885654 | 1.7312604 | 2.0926706 | 2.4943871 | 2.4943871 |
| mmu-miR-92a-3p.iso.t5:0.t3:T.ad:0.mm:0 | 25826.04849 | 0.0024922 | 0.1148568 | 307.8952 | 0 | 0 | mmu-miR-92a-3p.iso.t5:0.t3:T.ad:0.mm:0 | mmu-miR-92a-3p.iso.t5:0.t3:T.ad:0.mm:0 | 0.1266860 | 1.1327519 | 1.3676340 | 1.0886733 | 0.6160221 | 1.3676340 |
| mmu-miR-142a-5p.iso.t5:CC.t3:t.ad:0.mm:0 | 606.16226 | 1.3471400 | 0.1817580 | 303.3488 | 0 | 0 | mmu-miR-142a-5p.iso.t5:CC.t3:t.ad:0.mm:0 | mmu-miR-142a-5p.iso.t5:CC.t3:t.ad:0.mm:0 | 2.1017335 | 1.1788563 | 1.8938661 | 2.7462601 | 2.5578597 | 2.7462601 |
Working with 1071 genes 
Analysis for clusters
## Comparison: fa_model_cluster {.tabset}
out of 587 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up) : 157, 27%
LFC < 0 (down) : 181, 31%
outliers [1] : 2, 0.34%
low counts [2] : 0, 0%
(mean count < 6)
[1] see ‘cooksCutoff’ argument of ?results
[2] see ‘independentFiltering’ argument of ?results
NULL
Differential expression file at: fa_model_cluster.tsv
Normalized counts matrix file at: fa_model_cluster_log2_counts.tsv
MA plot plot
Volcano plot
QC for DE genes p-values/variance
Most significand, FDR< 0.05 and log2FC > 1 : 178
Plots most significand
Plot top 9 genes
Top DE genes
| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | symbol | description | Day14vsDay0 | Day1vsDay0 | Day2vsDay0 | Day3vsDay0 | Day7vsDay0 | absMaxLog2FC | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 433 | 2249.48322 | 0.9070674 | 0.3732575 | 222.37775 | 0 | 0 | 433 | 433 | 1.5714264 | 4.4169261 | 3.9961329 | 3.0406021 | 1.4994816 | 4.4169261 |
| 524 | 1825.59642 | 1.4928244 | 0.2247476 | 199.26349 | 0 | 0 | 524 | 524 | 2.5176476 | 0.7171127 | 1.3548461 | 2.3580632 | 2.4769055 | 2.5176476 |
| 581 | 830.92108 | 0.0551098 | 0.1808680 | 187.59921 | 0 | 0 | 581 | 581 | 0.3845358 | 1.6897462 | 1.5958847 | 0.9544170 | 0.6051035 | 1.6897462 |
| 10 | 248.67918 | 0.4301422 | 0.2060157 | 163.91234 | 0 | 0 | 10 | 10 | 1.2873803 | 1.4984656 | 1.6483184 | 1.7704845 | 2.0143328 | 2.0143328 |
| 143 | 61.38041 | 2.0475255 | 0.5029248 | 142.34243 | 0 | 0 | 143 | 143 | 3.0424560 | 0.7118289 | 3.1930821 | 3.9497840 | 3.9643826 | 3.9643826 |
| 343 | 64.55927 | 1.9278647 | 0.6809845 | 116.36999 | 0 | 0 | 343 | 343 | 1.9666072 | 5.1165617 | 4.7747046 | 3.7541310 | 2.1610405 | 5.1165617 |
| 209 | 91487.78417 | -0.3005822 | 0.1714544 | 107.66715 | 0 | 0 | 209 | 209 | -0.7211153 | -1.0813466 | -1.2883259 | -1.2687378 | -1.0533429 | 1.2883259 |
| 352 | 234955.42108 | 0.4043253 | 0.2683826 | 107.35545 | 0 | 0 | 352 | 352 | 1.2836260 | 1.5718652 | 2.1898987 | 2.0069401 | 2.0910592 | 2.1898987 |
| 17 | 158.85562 | 0.0399798 | 0.3281629 | 102.62231 | 0 | 0 | 17 | 17 | 0.7545601 | 1.2153195 | 2.1486236 | 2.1108204 | 1.8672980 | 2.1486236 |
| 450 | 135.84650 | 0.7362333 | 0.3167871 | 102.28819 | 0 | 0 | 450 | 450 | 1.5572398 | 0.2354885 | 1.3871195 | 2.1389756 | 2.2574049 | 2.2574049 |
| 376 | 213.56965 | 1.7275483 | 0.5997336 | 101.99441 | 0 | 0 | 376 | 376 | 2.0418641 | 4.4838385 | 4.7469158 | 4.7586558 | 2.7714175 | 4.7586558 |
| 12 | 272.48124 | -0.7432530 | 0.3095413 | 101.31684 | 0 | 0 | 12 | 12 | -1.7948377 | -1.2281486 | -1.6316536 | -2.0856325 | -2.7247396 | 2.7247396 |
| 11 | 7222.51936 | -0.3761254 | 0.2352652 | 90.01777 | 0 | 0 | 11 | 11 | -1.2622680 | -0.5538625 | -0.8623613 | -1.3182918 | -1.9443384 | 1.9443384 |
| 323 | 203.10656 | 0.0512942 | 0.3011742 | 88.51524 | 0 | 0 | 323 | 323 | 0.3118882 | 1.5420878 | 1.7928676 | 1.6646676 | 1.4653415 | 1.7928676 |
| 576 | 64.89637 | 0.2575567 | 0.5076091 | 88.65939 | 0 | 0 | 576 | 576 | 0.3177388 | 2.9555556 | 2.6581699 | 1.6229509 | 0.5102446 | 2.9555556 |
| 182 | 1348.14078 | 0.6991956 | 0.2707282 | 82.40146 | 0 | 0 | 182 | 182 | 0.6959874 | -1.0719157 | -1.0462163 | -0.2446071 | 0.2105213 | 1.0719157 |
| 387 | 133.43965 | 0.6631465 | 0.2871488 | 80.42204 | 0 | 0 | 387 | 387 | 1.6993664 | 1.6947198 | 1.3250564 | 1.9442881 | 1.9834675 | 1.9834675 |
| 142 | 5353.05737 | 0.0412670 | 0.1113550 | 79.01163 | 0 | 0 | 142 | 142 | 0.0445159 | -0.5129584 | -0.5877018 | -0.4413173 | -0.0035560 | 0.5877018 |
| 13 | 776.45634 | 1.0674236 | 0.3361205 | 78.34878 | 0 | 0 | 13 | 13 | 1.9435945 | 0.1130401 | 1.4074679 | 2.0754668 | 2.1628673 | 2.1628673 |
| 320 | 165.18074 | 1.0760742 | 0.4182942 | 78.22436 | 0 | 0 | 320 | 320 | 2.1496170 | 2.4107670 | 2.9185996 | 2.9433578 | 2.9779445 | 2.9779445 |
Working with 178 genes 
Files
Files generated contains raw count, normalized counts, log2 normalized counts and DESeq2 results.
R Session Info
(useful if replicating these results)
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid parallel stats4 methods stats graphics grDevices
[8] utils datasets base
other attached packages:
[1] vsn_3.40.0 edgeR_3.14.0
[3] limma_3.28.4 DEGreport_1.5.0
[5] quantreg_5.24 SparseM_1.7
[7] org.Mm.eg.db_3.3.0 AnnotationDbi_1.34.2
[9] myRfunctions_0.1 cluster_2.0.4
[11] pheatmap_1.0.8 isomiRs_0.99.13
[13] DiscriMiner_0.1-29 dplyr_0.4.3
[15] devtools_1.11.1 gridExtra_2.2.1
[17] gtools_3.5.0 CHBUtils_0.1
[19] genefilter_1.54.2 DESeq2_1.12.2
[21] SummarizedExperiment_1.2.2 Biobase_2.32.0
[23] GenomicRanges_1.24.0 GenomeInfoDb_1.8.1
[25] IRanges_2.6.0 S4Vectors_0.10.0
[27] BiocGenerics_0.18.0 reshape_0.8.5
[29] ggplot2_2.1.0 knitr_1.13
[31] rmarkdown_0.9.6 BiocInstaller_1.22.2
loaded via a namespace (and not attached):
[1] bitops_1.0-6 RColorBrewer_1.1-2 tools_3.3.0
[4] R6_2.1.2 affyio_1.42.0 rpart_4.1-10
[7] KernSmooth_2.23-15 Hmisc_3.17-4 DBI_0.4-1
[10] lazyeval_0.1.10 colorspace_1.2-6 nnet_7.3-12
[13] withr_1.0.1 GGally_1.0.1 Nozzle.R1_1.1-1
[16] preprocessCore_1.34.0 chron_2.3-47 formatR_1.4
[19] logging_0.7-103 labeling_0.3 caTools_1.17.1
[22] scales_0.4.0 affy_1.50.0 stringr_1.0.0
[25] digest_0.6.9 foreign_0.8-66 XVector_0.12.0
[28] htmltools_0.3.5 highr_0.6 RSQLite_1.0.0
[31] BiocParallel_1.6.2 acepack_1.3-3.3 magrittr_1.5
[34] Formula_1.2-1 Matrix_1.2-6 Rcpp_0.12.5
[37] munsell_0.4.3 stringi_1.0-1 yaml_2.1.13
[40] zlibbioc_1.18.0 gplots_3.0.1 plyr_1.8.3
[43] gdata_2.17.0 lattice_0.20-33 splines_3.3.0
[46] annotate_1.50.0 locfit_1.5-9.1 geneplotter_1.50.0
[49] codetools_0.2-14 XML_3.98-1.4 evaluate_0.9
[52] latticeExtra_0.6-28 data.table_1.9.6 MatrixModels_0.4-1
[55] gtable_0.2.0 tidyr_0.4.1 assertthat_0.1
[58] xtable_1.8-2 coda_0.18-1 survival_2.39-4
[61] memoise_1.0.0